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Irys® User Guide

07/10/2015

43

For Research Use Only. Not Intended For Diagnostic Purposes.

Figure 47: Custom Recipe is saved

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Summary of Contents for Irys

Page 1: ...Irys User Guide Document Number 30047 Document Revision A 07 28 2015 For Research Use Only Not Intended For Diagnostic Purposes Copyright 2015 BioNano Genomics Inc All Rights Reserved...

Page 2: ...rys ICS Main Screen Overview 14 Select User Screen 14 Chapter 3 Starting a Project 15 3 1 Irys System Project Workflow Overview 15 3 2 Sample Preparation Summary 15 IrysPrep Plug Lysis Long DNA Isolat...

Page 3: ...3 Initial Loading 34 Loading Step Concentration 35 Loading Step Spike 35 Loading Step Bump 36 Concentration Time Optimization 37 Loading Step Bump Time Optimization 37 Selecting Yes Pathway 39 Load T...

Page 4: ...ITH RESPECT TO THIS DOCUMENT EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE TO THE FULLEST EXTENT ALLOWED BY LAW IN NO EVENT SHALL BIONA...

Page 5: ...Date Summary Initial Release 07 28 2015 Released per CO 0131 Created a reformatted rebranded workflow styled Irys User Guide Replaces PN 30028 V1 6 New Features include Generate Optimized Recipe crea...

Page 6: ...paper or other matte surfaces are not harmful Protective eyewear is typically required where direct viewing of a class 3B laser beam may occur Class 3B lasers must be equipped with a key switch and a...

Page 7: ...Performed on the Irys 3 Molecule imaging Performed on the Irys 4 Data viewing and genome analysis Performed using IrysView 5 Data analysis Data analysis starts with AutoDetect the image detection soft...

Page 8: ...ids the complications of sample contamination background fluorescence and flowcell clogging and reduces data collection time And with thousands of identical parallel NanoChannels in each flowcell tens...

Page 9: ...be manually opened Right Side Power button The ON OFF button is located on the right hand side of the instrument USB Two USB 2 0 ports are located on the right hand side next to the power button Fiel...

Page 10: ...se EM CCD camera EM CCD camera has single photon detection capability combined with 90 QE quantum efficiency This frame transfer format delivers unequalled thermoelectric cooling industry lowest clock...

Page 11: ...ol the motion of molecules in the NanoChannels using electric fields 1 3 Irys Workstation Configuration Data Network Connections and Power Your information technology IT resource is responsible for Pr...

Page 12: ...ormance testing to ensure proper installation Calibration protocols and setting adjustments are performed during the installation and training sessions Note Do not attempt to move the instrument witho...

Page 13: ...enough material to perform 10 1X nick label repair stain reactions each requires 300 ng of raw DNA Table 8 IrysPrep Cat Product RE 011 10 IrysPrep 1 Color Assembly Reagent Kit 10 reaction RE 111 10 Ir...

Page 14: ...ion was in use The green check mark changes to a red exclamation mark or an hour glass to communicate when the instruments status changes For more information see the Troubleshooting section The Event...

Page 15: ...lity as the run proceeds 5 Data Analysis After the run completes the IrysChip is removed and the sample data are exported off Irys to a workstation for further analysis with IrysView and IrysSolve sof...

Page 16: ...erforming the run Once warmed dry off any moisture on the chip packaging before removing the chip Preparing IrysChip 1 Allow the IrysChip to warm up in its pouch and allow it to equilibrate to room te...

Page 17: ...a boot up sequence and launch to the LCD s desktop Select the Irys Instrument Control Software ICS application icon located on the desktop to launch Irys ICS Upon launching Irys ICS the system will p...

Page 18: ...window will ask for the password Figure 9 Select User Screen Figure 10 Enter Password optional Entering the incorrect password will deny access If the user does not require a password Irys will autom...

Page 19: ...equire network connectivity in order to export data to remote locations 2 Second Export Directory This location is the backup location Irys ICS will attempt to export data to when unable to export to...

Page 20: ...from the Select User screen to the Load Sample screen while the system calibrates 2 The XY Stage will eject and the Objective will rise Figure 12 Proceed to Load Sample Screen 4 1 Loading the Sample...

Page 21: ...e IrysChip Align the tip over the respective Inlet well and slowly depress the plunger until the bottom of the Inlet well is coated with sample solution Then slowly dispense the remainder of the sampl...

Page 22: ...s described in the Load Inlet section 2 Select the respective Load Outlet checkbox when complete No 2 minute timer is necessary Note Use the same NLRS reaction for both Inlet and Outlet wells of the s...

Page 23: ...at does not run down the side of the lens 5 Select the Oil Objective checkbox when finished oiling the Objective Figure 17 Load Sample Screen Complete Forward 1 After all required tasks are complete p...

Page 24: ...e IrysChip barcode and moves the workflow to the Focus Register screen a If unable to read the barcode because of smeared ink or missing IrysChip Irys will prompt the user to enter the barcode Part Nu...

Page 25: ...i If so press Reoil Objective Then follow the steps for cleaning and oiling the Objective Then press the Retract Stage button previously the Reoil button to initiate the automatic focusing process ag...

Page 26: ...late below the base recipes in alphabetical order Note Users may edit non default recipes by clicking on the recipe name A popup window opens up that allows the user to edit the recipe s concentration...

Page 27: ...concentration should be 5 ng l for optimal performance See the IrysPrep NLRS Experienced User Card PN 30024 5 Press the Forward button to go to either the Optimized Recipe or the Scanning Flowcell sc...

Page 28: ...the XY Stage to the load position a Promptly clean the oil from the Objective and the underside of the IrysChip cartridge b Rehydrate the sample with deionized water until the sample is flush with the...

Page 29: ...7 Clean The Clean screen outlines the tasks the user must follow in order to prepare the instrument for another run or for shutdown When entering this screen the XY Stage will eject and the Objective...

Page 30: ...o eject the XY Stage and dry the electrodes It is recommended that a user stand by for this task as solution may drip from the electrodes A timer of five minutes will begin once the button in pressed...

Page 31: ...cipe B from the Select Recipe screen By selecting Generate Optimized Recipe A or B the option to configure the flowcell s settings become available similar to selecting a base recipe Users may select...

Page 32: ...Note The user can exit Generate Optimized Recipe by pressing the Back arrow button to return to the Select Recipe screen or the Exit button to return to the Select User screen If the user was creating...

Page 33: ...sabled and the live image will indicate Camera OFF showing the last image taken by the camera There are some restrictions on vertical movements E Flowcell This displays the flowcell being used to gene...

Page 34: ...focus and optimization stage Figure 29 Focusing Step 3 Initial Loading The three parts to the Initial Loading step are Concentration Spike Bump After focus is achieved on the flowcell the Concentrati...

Page 35: ...ys guides the user through Concentration optimization Irys asks the user to press the OK button each time they see a vertical stream of DNA entering the leakage zone Pressing OK will decrease the forc...

Page 36: ...complete the bump measurement The number of elapsed seconds for the DNA to reach the target zone is recorded as a Bump Time Measurement Trial If the user does not press the OK button indicating DNA h...

Page 37: ...entration Time Optimization Note The live image remains active camera ON during Concentration Time Optimization so that the user can move horizontally along the IrysChip view to more accurately assess...

Page 38: ...onal one minute preparation step Up to four of the most recent Bump Time measurements are displayed under Recorded Bump Time s and Optimized Bump Time is displayed as an average of all recorded Bump T...

Page 39: ...d to the load position Note The amount of time it takes to perform the intermediate loading steps depends on which Base Recipe was used and can take up to 15 minutes Figure 39 Intermediate Loading Ste...

Page 40: ...igure 41 Optimized Load Time Measurement Users are then asked if the DNA loaded successfully Note The live image remains active Camera ON during this step so that the user can move horizontally along...

Page 41: ...view and the images are then compiled into a mosaic showing the entire array and marking the entrance and exit Figure 43 Imaging Example Scan Figure 44 Assembling Mosaic Selecting No Pathway By press...

Page 42: ...st text box Pressing the Yes button saves the recipe while pressing the No button returns the user to the Select Recipe screen If the recipe is saved it will be also be available in the Select Recipe...

Page 43: ...Irys User Guide 07 10 2015 43 For Research Use Only Not Intended For Diagnostic Purposes Figure 47 Custom Recipe is saved...

Page 44: ...ected network storage location during and after the run 2 To set or change the server export location press the User Settings button Type the drive and directory for the primary data export location i...

Page 45: ...leakage into the instrument Please see training video for reference at http www bionanogenomics com support training e Cleaning electrodes after every run is mandatory to prevent buffer component cont...

Page 46: ...se housing circled in red on the rear right of the instrument next to the power cable Figure 48 Fuse Location 2 Turn instrument power off and unplug the power cable 3 Pull on the tab on the left side...

Page 47: ...e system using an external keyboard and mouse to control system 2 Cycle power to instrument to reboot try touch screen again 3 If re booting does not correct the problem contact Customer Support LCD i...

Page 48: ...ch capabilities This button will shut down the system software from the Select User screen This button will return to the Select User screen from any other screen This status icon indicates that the s...

Page 49: ...disposable cartridge that contains a silicon chip with 2 embedded NanoChannel array flowcells each with an inlet and outlet well 4 NanoChannel array the location within the IrysChip that linearizes t...

Page 50: ...e Metro PCS mymetropcs com T Mobile tmomail net Verizon Wireless vtext com AT T txt att net Sprint PCS messaging sprintpcs com Nextel messaging nextel com Cricket sms mycricket com US Cellular email u...

Page 51: ...s user documentation MSDSs certificates of analysis frequently asked questions and other related documents from www bionanogenomics com support or by request through e mail and telephone To contact Te...

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